Additional file 4 of Up-regulation of apoptotic- and cell survival-related gene pathways following exposures of western corn rootworm to B. thuringiensis crystalline pesticidal proteins in transgenic maize roots

Additional file 4: Supplementary Table S3. Transcripts with significant differences in read counts (expression) between Diabrotica virgifera virgifera larvae feeding on transgenic maize expressing the insecticidal B. thuringiensis (Bt) Cry3Bb1 toxin (T8; Table 2) compared to control non-Bt maize (T7). For each transcript, indication of differential expression also being shared when larvae were exposed to Heterorhabditis bacteriophora (Hb) and Metarhizium anisopliae (Ma) is indicated with a “1”. Standard output are shown for DESeq2 (baseMean = the average of the normalized counts taken over all samples; log2FoldChange = log2 fold change between the groups; lfcSE = standard error of the log2FoldChange; stat = Wald statistic; pvalue = Wald test P-value; BH_padj = Benjamini-Hochberg adjusted p-value) and EdgeR (logFC = log2 fold change between the groups; logCPM = the average log2-counts-per-million; PValue = the two-sided P-value; BF_FDR = Bonferroni adjusted P-value). Lack of significance for any given transcript in DESeq2 or EdgeR results shown as “-”. The 1055 transcripts differentially expressed in both DESeq2 and EdgeR estimates are shown above the horizonal line. Transcript annotations include presence (Y) or absence (N) of signal_peptide probability (signalp_prob) threshold of > 0.700 shown only for “complete” proteins (match length = 1.0 to Drosophila melanogaster (Dm) or Trobiolium castaneum (Tc) protein models). PFAMSCAN_PfamA search results (format transcript query start, transcript query end: frame, strand (+ or -), range of hit to PFAM domain/PFAM domain name/ E-value/percent identity). Predicted protein information given (transcript start: transcript end: frame: strand (+ or -): amino acid sequence). BLASTx query results to indicated databases shown in standard output format with “/” indicating no values for queries receiving of hits. The 9 transcripts in blue italicized text are putatively derived from Hb or Ma.